Analysis of areal markers

p_load(tidyverse)

remotes::install_github("federicomarini/GeneTonic", 
                        dependencies = TRUE, build_vignettes = TRUE)

BiocManager::install("clusterProfiler")
BiocManager::install("pathview")
BiocManager::install("enrichplot")
library(clusterProfiler)
library(enrichplot)

p_load(biomaRt)

listMarts()

ensembl <- useMart("ensembl")
ensembl <- useDataset("hsapiens_gene_ensembl", mart = ensembl)

listDatasets(ensembl)

listAttributes(ensembl) %>% filter(! name %>% str_detect("homolog"))

searchAttributes(mart = ensembl, pattern = "GO")

genes 

$by_area_stage

$by_area

NA

goids <- getBM(attributes = c('hgnc_symbol', 'description', 'name_1006', 'definition_1006', 'go_id','namespace_1003'), 
              filters = 'hgnc_symbol', 
              values = genes, 
              mart = ensembl)

goids %>% as_tibble %>% dplyr::select(hgnc_symbol, description, name_1006, definition_1006, go_id, namespace_1003) %>% filter(namespace_1003 %in% c("molecular_function", "biological_process"))

goids %>% count(name_1006) %>% arrange(desc(n))

goids %>% filter(name_1006 %>% str_detect("transcription")) %>% distinct(hgnc_symbol, name_1006, .keep_all = TRUE)

Categories with the word ‘transcription’

goids %>% filter(name_1006 %>% str_detect("transcription")) %>% distinct(hgnc_symbol, name_1006, .keep_all = TRUE) %>% count(name_1006)

goids %>% filter(name_1006 %>% str_detect("transcription")) %>% distinct(hgnc_symbol, name_1006, .keep_all = TRUE) %>% 
  ggplot() + geom_tile(aes(y = name_1006, x = as_factor(hgnc_symbol), fill = name_1006))

Radial glia: PFC: all marker genes

goids_x <- getBM(attributes = c('hgnc_symbol', 'description', 
                                'name_1006', 'definition_1006', 'go_id',
                                'namespace_1003'), 
              filters = 'hgnc_symbol', 
              values = x, 
              mart = ensembl)

Error in martCheck(mart) : object 'ensembl' not found

    dplyr::select(hgnc_symbol, name_1006, n, description, everything())

Error in dplyr::select(hgnc_symbol, name_1006, n, description, everything()) : 
  object 'hgnc_symbol' not found

tf_cofactors <- read_tsv("animalDB/Homo_sapiens_TF_cofactors.txt") %>% set_names(tolower(names(.)))

Parsed with column specification:
cols(
  Species = col_character(),
  Symbol = col_character(),
  Ensembl = col_character(),
  Family = col_character(),
  `Entrez ID` = col_character()
)